[Psidev-pi-dev] storing intermediate results in mzML

[Richard S. <r.a...@ru...>]

Dear all,

I'm writing a metabolomics Java library for my processing software 
targeted towards high resolution LC/MS data (components like: peak 
picking, noise detection, etc). The basic element for this library is a 
mass chromatogram (x-axis time, y-axis intensity). In order to deal with 
the size of the datasets, enable other people to easily write 
components, etc. an intermediate file format is required. I've already 
defined one myself to see what would be required for a really dynamic 
pipeline and created a library on top of it. In order to hop on the 
international standards bandwagon I would off course like to move to a 
recognized standard like mzML. However, this _seems_ to fall short of my 
requirements. I've been browsing through this list and the standards 
document and tried to implement something, but I can't seem to figure 
out how to approach this.

What I would like to be able to do is store the following pieces of 
information:

- Multiple runs in a single file
 From the specification document: "A run in mzML should correspond to a 
single, consecutive and coherent set of scans on an instrument". This 
means that I essentially can only store data from a single raw file? I 
would like to do mix-models (see sets).

- MassChromatograms (single mass)
I would like to ubiquitously store mass chromatograms picked from the 
raw data. This means that both mass chromatograms made from centroid as 
well as profile data need to be stored. There is the option to store 
chromatogram data, but this seems limited to '2D' data where mass 
chromatogram data build with profile data needs '3D' data. In order to 
solve this the accession="MS:1000627" name="selected ion current 
chromatogram" needs sub-children? Or can it be set globally in the 
header or run, but then I would like to be able to mix models (see sets).

- BackgroundIons
The use of background ions are part of the pipeline. To store this an 
addition to the CV needs to be made.
 name: backgroundion chromatogram
 is_a: chromatogram type (MS:1000626)
 definition: chromatogram created by creating an array of a ubiquitously 
present mass.

- sets
The goal of the pipeline is to combine information from lots of 
measurements (biological, technical replicates, different machines, etc) 
and do perform various analysis methods. This means for example that 
background ions or mass chromatograms from various measurements need to 
be combined into sets. Different operations and visualizations are then 
possible on the data stored in the files. The same as the different runs 
applies here. Another option would be to make sets of sets, which means 
that the relation needs to be recursive. I can probably solve some of 
the issues with id-fields, but that would make it hard to parse for 
other people and sort of rule out the recursive relation.


I can off course solve a lot with the use of userParam tags, but then 
other people will have a hard time reading the data. Another thing, I 
once heard somebody mention AnalysisML to be something along these 
lines, however this project seems to have suffered a fatal end as I 
cannot find anything? Am I trying to use mzML outside of its boundries? 
If so, is a viable alternative available which I have so far been unable 
to find?


Cheers,
Richard

-- 
Drs. ing. RA Scheltema    Groningen Bioinformatics Centre
Tel: +31 50 363 8078      Kerklaan 30
Fax: +31 50 363 7976      9751 NN, Haren
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